8ZA9: HBMBPP-BTN2A1-BTN3A1 complex

Cryo-EM structure of HBMBPP-BTN2A1-BTN3A1 complex. Determined by electron microscopy at 3.7 Å resolution. Released 30 Apr 2025.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 15,398
Mol. weight: 222.78 kDa
Ligands: H6P
Released: 30 Apr 2025

Explore 8ZA9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZA9 contains 37 α-helices and 173 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 7 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	11-14	4	2
α-helix	22	1
β-strand	23	1	3
β-strand	24	1	1
β-strand	35-40	6	2
β-strand	46-49	4	2
α-helix	57-59	3
β-strand	68-69	2	4
β-strand	80	1	3
β-strand	83-84	2	4
α-helix	89-91	3
β-strand	93-100	8	2
β-strand	101	1	5
β-strand	104	1	5
β-strand	107-115	9	2
β-strand	116	1	6
β-strand	121-129	9	7
β-strand	132-142	11	7
β-strand	143	1	6
β-strand	147-148	2	8
β-strand	151	1	9
β-strand	157	1	9
β-strand	161-162	2	7
α-helix	163-165	3
β-strand	166-167	2	7
β-strand	173-181	9	7
β-strand	189-190	2	9
β-strand	193-194	2	8
β-strand	201-202	2	8
β-strand	205-206	2	9
α-helix	218-290	73
α-helix	300-304	5
β-strand	309-310	2	10
β-strand	315	1	11
β-strand	324-326	3	12
β-strand	333-335	3	12
α-helix	342-344	3
β-strand	354-356	3	13
β-strand	357	1	11
β-strand	361	1	13
β-strand	365-371	7	10
β-strand	379-384	6	13
β-strand	402-407	6	13
β-strand	411-414	4	13
β-strand	420-421	2	13
β-strand	430-436	7	10
β-strand	442-446	5	10
β-strand	451-456	6	10
β-strand	465-470	6	13
β-strand	480-481	2	10

Chain D: 8 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	37
α-helix	10	1
β-strand	11-14	4	38
β-strand	19-23	5	39
β-strand	24-26	3	37
β-strand	35-40	6	40
β-strand	46-51	6	40
β-strand	54-56	3	40
α-helix	62-64	3
β-strand	68-71	4	39
β-strand	80-84	5	39
β-strand	95-101	7	40
β-strand	104-110	7	40
β-strand	112-115	4	38
β-strand	116	1	41
β-strand	122-128	7	9
β-strand	133-138	6	9
β-strand	142	1	42
β-strand	143	1	41
α-helix	145-146	2
β-strand	147-152	6	7
β-strand	157	1	7
β-strand	161-162	2	43
α-helix	163-165	3
β-strand	166-167	2	42
β-strand	173-174	2	42
β-strand	176	1	9
β-strand	177-178	2	43
β-strand	179-181	3	9
β-strand	189-194	6	7
β-strand	201-208	8	7
α-helix	216-289	74
α-helix	300-303	4
β-strand	310	1	44
β-strand	326	1	44
β-strand	332-333	2	44
β-strand	365-371	7	44
β-strand	380-383	4	45
α-helix	397-399	3
β-strand	401-407	7	45
β-strand	411-415	5	45
β-strand	420-421	2	45
β-strand	430-436	7	44
β-strand	441-446	6	44
β-strand	454-456	3	44
β-strand	466-469	4	45
β-strand	479-481	3	44
α-helix	482-483	2

Chain E: 13 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	14
α-helix	10	1
β-strand	11-14	4	15
β-strand	19-23	5	16
β-strand	24	1	14
β-strand	36-39	4	17
β-strand	46	1	18
β-strand	48-51	4	17
β-strand	54-56	3	17
β-strand	60	1	18
α-helix	62-64	3
β-strand	70-74	5	16
β-strand	79-84	6	16
α-helix	89-91	3
β-strand	93	1	15
β-strand	96-101	6	17
β-strand	104-109	6	17
β-strand	112-115	4	15
β-strand	116	1	19
α-helix	119-121	3
β-strand	122-129	8	20
β-strand	132-142	11	20
β-strand	143	1	19
β-strand	147-151	5	21
β-strand	157-158	2	21
α-helix	159-160	2
β-strand	162-165	4	20
β-strand	173-178	6	20
β-strand	180-181	2	20
β-strand	188-194	7	21
β-strand	201-207	7	21
α-helix	208-209	2
α-helix	210-212	3
α-helix	215-217	3
α-helix	218-291	74
β-strand	297-299	3	22
β-strand	304	1	23
β-strand	313-315	3	22
β-strand	321-324	4	22
β-strand	346-348	3	24
β-strand	349	1	23
β-strand	353	1	24
β-strand	357-363	7	22
β-strand	370-376	7	24
α-helix	389-391	3
β-strand	393-397	5	24
β-strand	398-399	2	25
β-strand	402-403	2	25
β-strand	421-427	7	22
α-helix	428-430	3
β-strand	432-437	6	22
β-strand	442-447	6	22
β-strand	456-462	7	24
α-helix	468	1
β-strand	469-471	3	22
α-helix	472-474	3
β-strand	488-489	2	22

Chain G: 9 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	26
β-strand	12-13	2	27
β-strand	19-23	5	28
β-strand	24-26	3	26
β-strand	35-39	5	29
β-strand	46	1	30
β-strand	48-51	4	29
β-strand	54-55	2	29
β-strand	60	1	30
β-strand	69	1	28
α-helix	75-77	3
β-strand	80-84	5	28
α-helix	89-91	3
β-strand	93-100	8	29
β-strand	106-112	7	29
β-strand	113-114	2	27
β-strand	116	1	31
α-helix	119-121	3
β-strand	122-129	8	32
β-strand	132-138	7	32
β-strand	139-142	4	33
β-strand	143	1	31
β-strand	147-151	5	34
β-strand	157	1	34
α-helix	158-160	3
β-strand	162-164	3	32
β-strand	167	1	33
β-strand	173-175	3	33
β-strand	176-181	6	32
β-strand	188-194	7	34
β-strand	201-207	7	34
α-helix	210-212	3
α-helix	222-252	31
α-helix	255-293	39
β-strand	297-299	3	22
β-strand	304	1	35
β-strand	313-315	3	22
β-strand	321-324	4	22
β-strand	346-348	3	36
β-strand	349	1	35
β-strand	353	1	36
β-strand	357-363	7	22
β-strand	370-376	7	36
β-strand	393-399	7	36
β-strand	402-404	3	36
β-strand	412	1	36
β-strand	421-427	7	22
β-strand	432-437	6	22
β-strand	442-446	5	22
α-helix	447-449	3
β-strand	456-462	7	36
β-strand	469-471	3	22
α-helix	472-474	3
β-strand	489	1	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Butyrophilin subfamily 3 member A1	C, D	protein	484	Homo sapiens	O00481 (AlphaFold model)
Butyrophilin subfamily 2 member A1	E, G	protein	499	Homo sapiens	Q7KYR7 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>8ZA9_1 Butyrophilin subfamily 3 member A1 (chains C, D)
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQ
SAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSD
LHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVI
MRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQRWIAALAGTLPVLLLLLGGAGYF
LWQQQEEKKTQFRKKKREQELREMAWSTMKQEQSTRVKLLEELRWRSIQYASRGERHSAY
NEWKKALFKPADVILDPKTANPILLVSEDQRSVQRAKEPQDLPDNPERFNWHYCVLGCES
FISGRHYWEVEVGDRKEWHIGVCSKNVQRKGWVKMTPENGFWTMGLTDGNKYRTLTEPRT
NLKLPKTPKKVGVFLDYETGDISFYNAVDGSHIHTFLDVSFSEALYPVFRILTLEPTALT
ICPA

Sequence of entity 2 (E, G), FASTA

>8ZA9_2 Butyrophilin subfamily 2 member A1 (chains E, G)
QFIVVGPTDPILATVGENTTLRCHLSPEKNAEDMEVRWFRSQFSPAVFVYKGGRERTEEQ
MEEYRGRTTFVSKDISRGSVALVIHNITAQENGTYRCYFQEGRSYDEAILHLVVAGLGSK
PLISMRGHEDGGIRLECISRGWYPKPLTVWRDPYGGVAPALKEVSMPDADGLFMVTTAVI
IRDKSVRNMSCSINNTLLGQKKESVIFIPESFMPSVSPCAVALPIIVVILMIPIAVCIYW
INKLQKEKKILSGEKEFERETREIALKELEKERVQKEEELQVKEKLQEELRWRRTFLHAV
DVVLDPDTAHPDLFLSEDRRSVRRCPFRHLGESVPDNPERFDSQPCVLGRESFASGKHYW
EVEVENVIEWTVGVCRDSVERKGEVLLIPQNGFWTLEMHKGQYRAVSSPDRILPLKESLC
RVGVFLDYEAGDVSFYNMRDRSHIYTCPRSAFSVPVRPFFRLGCEDSPIFICPALTGANG
VTVPEEGLTLHRVGTHQSL

Ligands and cofactors

ID	Name	Formula	Copies
H6P	(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate	C5 H12 O8 P2	1

Primary citation

Phosphoantigen-induced inside-out stabilization of butyrophilin receptor complexes drives dimerization-dependent gamma delta TCR activation. Zhu, Y., Gao, W., Zheng, J. et al. Immunity (2025) 58:1646-1659.e5. DOI 10.1016/j.immuni.2025.04.012 · PubMed

Other PDB entries of the same protein (UniProt O00481 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ITA 1.2 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 mutant
6ISM 1.25 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 mutant
8IZE 1.4 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with 4-HMBPP
4N7I 1.4 Å, Crystal Structure of Intracellular B30.2 Domain of BTN3A1
4N7U 1.46 Å, Crystal Structure of Intracellular B30.2 Domain of BTN3A1 in Complex with CHDMAPP
5LYG 1.6 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 bound to malonate
8IZG 1.6 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with 5-HMBPP
5LYK 1.7 Å, Crystal structure of intracellular B30.2 domain of BTN3A1 bound to citrate
8IXV 1.72 Å, Crystal structure of intracellular B30.2 domain of BTN3A in complex with 2Cl-HMBPP
4K55 1.91 Å, Structure of the extracellular domain of butyrophilin BTN3A1 in complex with…
5HM7 1.93 Å, The Intracellular domain of Butyrophilin 3A1 protein
4F80 1.94 Å, Crystal Structure of the human BTN3A1 ectodomain

Browse structure collections

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